data_3MDJ # _model_server_result.job_id Wj72S8vo3CWIDIYXSVPTqQ _model_server_result.datetime_utc '2024-12-24 18:30:19' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3mdj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1001}' # _entry.id 3MDJ # _exptl.entry_id 3MDJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.373 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.59 _cell.angle_gamma 90 _cell.entry_id 3MDJ _cell.length_a 71.029 _cell.length_b 234.635 _cell.length_c 95.86 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MDJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G,H,I,J 1 1 B,E,K,L,M 2 1 C,F,N,O 3 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 H N N ? 5 L N N ? 5 O N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n D NAG 1 D 1 NAG A 5001 NAG 2 n D NAG 2 D 2 NAG A 5002 NAG 2 n D BMA 3 D 3 BMA A 5003 BMA 2 n D MAN 4 D 4 MAN A 5004 MAN 2 n D MAN 5 D 5 MAN A 5005 MAN 3 n E NAG 1 E 1 NAG B 5001 NAG 3 n E NAG 2 E 2 NAG B 5002 NAG 2 n F NAG 1 F 1 NAG C 5001 NAG 2 n F NAG 2 F 2 NAG C 5002 NAG 2 n F BMA 3 F 3 BMA C 5003 BMA 2 n F MAN 4 F 4 MAN C 5004 MAN 2 n F MAN 5 F 5 MAN C 5005 MAN # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 368 A CYS 404 1_555 A SG CYS 407 A CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 700 A CYS 736 1_555 A SG CYS 707 A CYS 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 368 B CYS 404 1_555 B SG CYS 407 B CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 700 B CYS 736 1_555 B SG CYS 707 B CYS 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? disulf ? disulf5 C SG CYS 368 C CYS 404 1_555 C SG CYS 407 C CYS 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 C SG CYS 700 C CYS 736 1_555 C SG CYS 707 C CYS 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 34 A ASN 70 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale2 A ND2 ASN 118 A ASN 154 1_555 I C1 NAG . A NAG 6000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? covale ? covale3 A ND2 ASN 724 A ASN 760 1_555 J C1 NAG . A NAG 6001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale4 B ND2 ASN 34 B ASN 70 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.498 ? covale ? covale5 B ND2 ASN 118 B ASN 154 1_555 M C1 NAG . B NAG 6000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.487 ? covale ? covale6 C ND2 ASN 34 C ASN 70 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale8 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale9 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale10 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale12 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale13 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale14 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale15 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? metalc ? metalc1 A NE2 HIS 317 A HIS 353 1_555 G ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc2 A NE2 HIS 321 A HIS 357 1_555 G ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc3 A OE1 GLU 340 A GLU 376 1_555 G ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc4 A OE2 GLU 340 A GLU 376 1_555 G ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc5 G ZN ZN . A ZN 1000 1_555 H O2 BES . A BES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 B NE2 HIS 317 B HIS 353 1_555 K ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc7 B NE2 HIS 321 B HIS 357 1_555 K ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc8 B OE1 GLU 340 B GLU 376 1_555 K ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc9 B OE2 GLU 340 B GLU 376 1_555 K ZN ZN . B ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc10 K ZN ZN . B ZN 1000 1_555 L O2 BES . B BES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc11 C NE2 HIS 317 C HIS 353 1_555 N ZN ZN . C ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc12 C NE2 HIS 321 C HIS 357 1_555 N ZN ZN . C ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc13 C OE1 GLU 340 C GLU 376 1_555 N ZN ZN . C ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc14 C OE2 GLU 340 C GLU 376 1_555 N ZN ZN . C ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc15 N ZN ZN . C ZN 1000 1_555 O O2 BES . C BES 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? # _chem_comp.formula 'C16 H24 N2 O4' _chem_comp.formula_weight 308.373 _chem_comp.id BES _chem_comp.mon_nstd_flag . _chem_comp.name '2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms BESTATIN # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N2 C1 BES sing 70 n n N2 HN21 BES sing 71 n n N2 HN22 BES sing 72 n n C1 C6 BES sing 73 n n C1 C2 BES sing 74 n n C1 H1 BES sing 75 n n C6 C7 BES sing 76 n n C6 H61 BES sing 77 n n C6 H62 BES sing 78 n n C7 C8 BES doub 79 n y C7 C12 BES sing 80 n y C8 C9 BES sing 81 n y C8 H8 BES sing 82 n n C12 C11 BES doub 83 n y C12 H12 BES sing 84 n n C9 C10 BES doub 85 n y C9 H9 BES sing 86 n n C11 C10 BES sing 87 n y C11 H11 BES sing 88 n n C10 H10 BES sing 89 n n C2 O2 BES sing 90 n n C2 C3 BES sing 91 n n C2 H2 BES sing 92 n n O2 HO2 BES sing 93 n n C3 O3 BES doub 94 n n C3 N1 BES sing 95 n n N1 C4 BES sing 96 n n N1 HN BES sing 97 n n C4 C13 BES sing 98 n n C4 C5 BES sing 99 n n C4 H4 BES sing 100 n n C13 C14 BES sing 101 n n C13 H131 BES sing 102 n n C13 H132 BES sing 103 n n C14 C15 BES sing 104 n n C14 C16 BES sing 105 n n C14 H14 BES sing 106 n n C15 H151 BES sing 107 n n C15 H152 BES sing 108 n n C15 H153 BES sing 109 n n C16 H161 BES sing 110 n n C16 H162 BES sing 111 n n C16 H163 BES sing 112 n n C5 O1 BES sing 113 n n C5 O4 BES doub 114 n n O1 HO1 BES sing 115 n n # _atom_sites.entry_id 3MDJ _atom_sites.fract_transf_matrix[1][1] 0.014079 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003403 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004262 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.010732 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code G 4 ZN A 1 1000 1000 ZN ZN . H 5 BES A 1 1001 1001 BES BES . I 6 NAG A 1 6000 6000 NAG NAG . J 6 NAG A 1 6001 6001 NAG NAG . K 4 ZN B 1 1000 1000 ZN ZN . L 5 BES B 1 1001 1001 BES BES . M 6 NAG B 1 6000 6000 NAG NAG . N 4 ZN C 1 1000 1000 ZN ZN . O 5 BES C 1 1001 1001 BES BES . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N2 BES . . . L 5 26.939 73.064 -61.29 1 218.71 ? N2 BES 1001 B 1 HETATM 2 C C1 BES . . . L 5 27.266 74.344 -61.925 1 185.05 ? C1 BES 1001 B 1 HETATM 3 C C6 BES . . . L 5 28.098 74.135 -63.183 1 172.14 ? C6 BES 1001 B 1 HETATM 4 C C7 BES . . . L 5 27.424 73.225 -64.195 1 169.09 ? C7 BES 1001 B 1 HETATM 5 C C8 BES . . . L 5 28.157 72.155 -64.69 1 180.13 ? C8 BES 1001 B 1 HETATM 6 C C12 BES . . . L 5 26.118 73.435 -64.614 1 156 ? C12 BES 1001 B 1 HETATM 7 C C9 BES . . . L 5 27.595 71.289 -65.614 1 177.21 ? C9 BES 1001 B 1 HETATM 8 C C11 BES . . . L 5 25.555 72.566 -65.539 1 155.26 ? C11 BES 1001 B 1 HETATM 9 C C10 BES . . . L 5 26.29 71.495 -66.038 1 168.25 ? C10 BES 1001 B 1 HETATM 10 C C2 BES . . . L 5 28.065 75.2 -60.953 1 159.12 ? C2 BES 1001 B 1 HETATM 11 O O2 BES . . . L 5 27.336 75.357 -59.739 1 121.36 ? O2 BES 1001 B 1 HETATM 12 C C3 BES . . . L 5 28.381 76.553 -61.581 1 173.05 ? C3 BES 1001 B 1 HETATM 13 O O3 BES . . . L 5 27.494 77.374 -61.803 1 206.58 ? O3 BES 1001 B 1 HETATM 14 N N1 BES . . . L 5 29.662 76.749 -61.881 1 139.56 ? N1 BES 1001 B 1 HETATM 15 C C4 BES . . . L 5 30.078 78.012 -62.486 1 137.02 ? C4 BES 1001 B 1 HETATM 16 C C13 BES . . . L 5 30.216 79.027 -61.355 1 122.86 ? C13 BES 1001 B 1 HETATM 17 C C14 BES . . . L 5 30.594 80.39 -61.92 1 146.17 ? C14 BES 1001 B 1 HETATM 18 C C15 BES . . . L 5 29.505 80.876 -62.88 1 124.69 ? C15 BES 1001 B 1 HETATM 19 C C16 BES . . . L 5 30.829 81.4 -60.798 1 156.71 ? C16 BES 1001 B 1 HETATM 20 C C5 BES . . . L 5 31.424 77.811 -63.185 1 167.02 ? C5 BES 1001 B 1 HETATM 21 O O1 BES . . . L 5 32.087 76.805 -62.855 1 183.72 ? O1 BES 1001 B 1 HETATM 22 O O4 BES . . . L 5 31.759 78.659 -64.042 1 177.68 ? O4 BES 1001 B 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #